In 1866 Graham was once again elected to the United States Senate, but because North Carolina had not yet been readmitted to the Union, he did not present his credentials. From 1867 to 1875 he was a member of the board of trustees of the Peabody Fund, which provided educational assistance to the post-Civil WarSouth. From 1873 to 1875 he was an arbitrator in the boundary line dispute between Virginia and Maryland. He died in Saratoga Springs, New York, and is buried in the Presbyterian Church Cemetery in Hillsborough.

One of Graham's sons, also named William A. Graham, became a state legislator and state agriculture commissioner. Two others, Augustus and John, also became politicians, while a daughter, Susan, married Walter Clark.